Variant report

Variant	rs2678091
Chromosome Location	chr5:118834606-118834607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118831350..118835449-chr5:118835713..118839843,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133835	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs161852	0.81[ASN][1000 genomes]
rs2257900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257901	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2259347	0.85[ASN][1000 genomes]
rs2451816	0.86[ASN][1000 genomes]
rs2459726	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs246965	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs246967	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2546210	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs25640	0.85[ASN][1000 genomes]
rs257970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257971	0.99[ASN][1000 genomes]
rs257972	0.86[ASN][1000 genomes]
rs257973	0.86[ASN][1000 genomes]
rs257974	0.86[ASN][1000 genomes]
rs257975	0.86[ASN][1000 genomes]
rs257976	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs26181	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs26184	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2636961	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2636962	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2636964	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636968	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2678074	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2678076	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs27938	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2945327	0.97[ASN][1000 genomes]
rs32659	0.99[ASN][1000 genomes]
rs32662	0.99[ASN][1000 genomes]
rs32663	0.99[ASN][1000 genomes]
rs32664	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs32665	0.99[ASN][1000 genomes]
rs35235684	0.96[ASN][1000 genomes]
rs382719	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3850202	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs39970	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs422297	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs426899	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs460274	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs463098	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2678091	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:118794800-118861200	Weak transcription	HSMM	muscle
3	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:118804800-118837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:118805200-118839400	Weak transcription	NHEK	skin
6	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
7	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
8	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
9	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
10	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
12	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
14	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
16	chr5:118809600-118838000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
18	chr5:118812000-118846400	Weak transcription	NHLF	lung
19	chr5:118814000-118838200	Weak transcription	Fetal Intestine Small	intestine
20	chr5:118814000-118845000	Weak transcription	Gastric	stomach
21	chr5:118814000-118845200	Weak transcription	Aorta	Aorta
22	chr5:118814800-118839400	Weak transcription	Right Ventricle	heart
23	chr5:118814800-118844800	Weak transcription	Lung	lung
24	chr5:118815400-118835400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:118815400-118839000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:118815800-118839000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:118815800-118845400	Weak transcription	HMEC	breast
28	chr5:118816000-118844000	Weak transcription	Hela-S3	cervix
29	chr5:118816000-118847000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:118816800-118837800	Strong transcription	Dnd41	blood
31	chr5:118816800-118839600	Strong transcription	Adipose Nuclei	Adipose
32	chr5:118817000-118837800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:118817000-118846400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr5:118817200-118839600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:118818400-118839600	Weak transcription	Fetal Kidney	kidney
36	chr5:118819000-118839200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:118819600-118844400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:118820000-118839000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:118820000-118839600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:118820200-118838600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:118820200-118846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:118820400-118838800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:118821000-118839600	Strong transcription	Liver	Liver
44	chr5:118821000-118843800	Weak transcription	NHDF-Ad	bronchial
45	chr5:118822000-118835600	Weak transcription	Brain Angular Gyrus	brain
46	chr5:118822000-118837200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr5:118823600-118837000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:118823800-118837400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr5:118824200-118838400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:118824400-118837000	Strong transcription	Placenta	Placenta

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